The large number of microbial species and their interactions has led to large uncertainties associated with predicted ecosystem functions based solely on taxonomic information. To overcome this challenge, we need to incorporate functional information on microbial traits to better understand ecosystem functioning. Although compared to plant ecology, microbial ecology remains behind in adopting functional-trait based approaches, large amounts of metagenomic information are currently generated. I contend that comparing species-level and community-level traits enables a deeper understanding of the evolutionary and ecological forces shaping biodiversity and ecosystem functioning.